A5038917449- Radiomics and Machine Learning in Medical Imaging
- AI in cancer detection
- Cancer Genomics and Diagnostics
- Colorectal Cancer Treatments and Studies
- Cancer Immunotherapy and Biomarkers
- RNA Research and Splicing
- Single-cell and spatial transcriptomics
- Acute Myeloid Leukemia Research
- RNA modifications and cancer
- Genetic factors in colorectal cancer
- Distributed and Parallel Computing Systems
- Chronic Lymphocytic Leukemia Research
- Advanced biosensing and bioanalysis techniques
- Cell Image Analysis Techniques
- Protein Degradation and Inhibitors
- RNA Interference and Gene Delivery
- Parallel Computing and Optimization Techniques
- RNA and protein synthesis mechanisms
- Advanced Data Storage Technologies
- Cytokine Signaling Pathways and Interactions
- Immune Cell Function and Interaction
- Advanced X-ray and CT Imaging
- Lymphoma Diagnosis and Treatment
- Multiple Myeloma Research and Treatments
- Epigenetics and DNA Methylation
Jackson Laboratory
2021-2025
Sage Bionetworks
2017-2024
Robert Bosch (Germany)
2024
Carestream (United States)
2023-2024
Washington University in St. Louis
2013-2021
Seattle University
2019
National Human Genome Research Institute
2016-2018
Cornell University
2005-2017
AtlantiCare
2017
Regional Medical Center
2017
Three experimental environments traditionally support network and distributed systems research: emulators, simulators, live networks. The continued use of multiple approaches highlights both the value inadequacy each. Netbed, a descendant Emulab, provides an experimentation facility that integrates these approaches, allowing researchers to configure access networks composed emulated, simulated, wide-area nodes links. Netbed's primary goals are ease use, control , realism achieved through...
The sensitivity of massively-parallel sequencing has confirmed that most cancers are oligoclonal, with subpopulations neoplastic cells harboring distinct mutations. A fine resolution view this clonal architecture provides insight into tumor heterogeneity, evolution, and treatment response, all which may have clinical implications. Single analysis already contributes to understanding these phenomena. However, cryptic subclones frequently revealed by additional patient samples (e.g., collected...
Next-generation sequencing has been used to infer the clonality of heterogeneous tumor samples. These analyses yield specific predictions—the population frequency individual clones, their genetic composition, and evolutionary relationships—which we set out test by cells from three subjects diagnosed with secondary acute myeloid leukemia, each whom had previously characterized whole genome unfractionated Single-cell mutation profiling strongly supported clonal architecture implied analysis...
mutation is a common canonical in colorectal cancer, found at differing frequencies all consensus molecular subtypes (CMS). The independent immunobiological impacts of RAS and CMS are unknown. Thus, we explored the effects
Abstract Somatic mutations in spliceosome genes are detectable ∼50% of patients with myelodysplastic syndromes (MDS). We hypothesize that cells harbouring gene have increased sensitivity to pharmacological perturbation the spliceosome. focus on mutant U2AF1 and utilize sudemycin compounds modulate pre-mRNA splicing. find haematopoietic expressing U2AF1(S34F), including primary patient cells, an vitro treatment relative controls. In vivo U2AF1(S34F) transgenic mice alters splicing reverts...
The Food and Drug Administration often requires postapproval studies to address issues such as optimal dosing, potential long-term side effects, use in children or confirm a drug's clinical benefit. But many of these aren't completed on time, if at all.
Tumor heterogeneity and evolution drive treatment resistance in metastatic colorectal cancer (mCRC). Patient-derived xenografts (PDXs) can model mCRC biology; however, their ability to accurately mimic human tumor is unclear. Current genomic studies have limited scope lack matched PDXs. Therefore, the landscape of its impact on metastasis PDXs remain undefined. We performed whole-genome, deep exome, targeted validation sequencing multiple primary regions, distant metastases, from 11 patients...
Aptamers are high-affinity ligands selected from DNA or RNA libraries via SELEX, a repetitive in vitro process of sequential selection and amplification steps. SELEX is more complicated than because the additional transcription reverse Here, we report new scheme, RAPID-SELEX (RNA Aptamer Isolation Dual-cycles SELEX), that simplifies this by systematically skipping unnecessary Using affinity microcolumns, were able to complete multiplex for protein targets, CHK2 UBLCP1, third time required...
The four-subunit Negative Elongation Factor (NELF) is a major regulator of RNA Polymerase II (Pol II) pausing. subunit NELF-E contains conserved Recognition Motif (RRM) and proposed to facilitate Poll pausing through its association with nascent transcribed RNA. However, conflicting ideas have emerged for the function binding activity. Here, we use in vitro selection strategies quantitative biochemistry identify characterize consensus element (NBE) that required sequence specific recognition...
Mechanisms of tissue stem cell (SC) quiescence control are important for normal homeostasis and preventing cancer. Cyclin-dependent kinase inhibitors (CDKis) known cycle progression. We document CDKis expression in vivo during hair follicle (HFSC) find p21 (cyclin-dependent inhibitor 1a, Cdkn1a), p57, p15 up-regulated at onset. appears HFSC timely onset quiescence. Conversely, we that Runx1 (runt related transcription factor 1), which is promoting proliferation, represses p21, p27, vivo....
Abstract Multiple myeloma (MM) is a disease of copy number variants (CNVs), chromosomal translocations, and single-nucleotide (SNVs). To enable integrative studies across these diverse mutation types, we developed capture-based sequencing platform to detect their occurrence in 465 genes altered MM used it sequence 95 primary tumor-normal pairs mean depth 104×. We detected cases hyperdiploidy (23%), deletions 1p (8%), 6q (21%), 8p (17%), 14q (16%), 16q (22%), 17p (4%), amplification 1q (19%)....
While the past decade has seen meaningful improvements in clinical outcomes for multiple myeloma patients, a subset of patients does not benefit from current therapeutics unclear reasons. Many gene expression-based models risk have been developed, but each model uses different combination genes and often involves assaying many making them difficult to implement. We organized Multiple Myeloma DREAM Challenge, crowdsourced effort develop rapid progression newly diagnosed benchmark these...
Abstract We evaluate deconvolution methods, which infer levels of immune infiltration from bulk expression tumor samples, through a community-wide DREAM Challenge. assess six published and 22 community-contributed methods using in vitro silico transcriptional profiles admixed cancer healthy cells. Several predict most cell types well, though they either were not trained to all functional CD8+ T states or do so with low accuracy. address this gap, including deep learning-based approach, whose...
Realizing that current file systems can not cope with the diverse requirements of wide-area collaborations, researchers have developed data access facilities to meet their needs. Recent work has focused on comprehensive architectures. In order fulfill evolving in this environment, we suggest a more fully-integrated architecture built upon fundamental tenets naming, security, scalability, extensibility, and adaptability. These form underpinning Legion File System (LegionFS). This paper...
Abstract Convolutional neural networks (CNNs) are revolutionizing digital pathology by enabling machine learning-based classification of a variety phenotypes from hematoxylin and eosin (H&E) whole slide images (WSIs), but the interpretation CNNs remains difficult. Most studies have considered interpretability in post hoc fashion, e.g. presenting example regions with strongly predicted class labels. However, such an approach does not explain biological features that contribute to correct...
We created the PDX Network (PDXNet) portal (https://portal.pdxnetwork.org/) to centralize access National Cancer Institute-funded PDXNet consortium resources, facilitate collaboration among researchers and make these data easily available for research. The includes sections analysis results, metrics activities, processing protocols training materials data. Currently, contains model information resources from 334 new models across 33 cancer types. Tissue samples of were deposited in NCI's...
The success of ns highlights the importance an infrastructure that enables efficient experimentation. Similarly, Netbed's automatic configuration and control emulated live network environments minimizes effort spent configuring running experiments. Learning from evolution these systems, in this paper we argue a wireless mobile experimental facility focusing on ease use accessibility will not only greatly lower barrier to research areas, but primary technical challenges can be overcome.The...